A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2024-11-07, 09:50 CET
based on data in:
/DKHC/scratch/markop/_p_Endophytes/_I_Bsubtilis/_S_NGS_mixed_cultures_exp2/_A_03_exp2-STAR_limma/output
General Statistics
| Sample Name | Total reads | Aligned | Aligned | Uniq aligned | Uniq aligned | Multimapped | Trimmed bases |
|---|---|---|---|---|---|---|---|
| BS830 | 21.8M | 19.9M | 91.0% | 18.9M | 86.7% | 0.9M | |
| BS830_1 | 0.5% | ||||||
| BS830_2 | 0.6% | ||||||
| BS831 | 22.2M | 20.6M | 92.5% | 19.7M | 88.3% | 0.9M | |
| BS831_1 | 0.5% | ||||||
| BS831_2 | 0.6% | ||||||
| BS832 | 21.3M | 19.4M | 91.1% | 18.6M | 87.1% | 0.9M | |
| BS832_1 | 0.5% | ||||||
| BS832_2 | 0.6% | ||||||
| BS833 | 20.6M | 18.9M | 91.8% | 18.1M | 88.0% | 0.8M | |
| BS833_1 | 0.5% | ||||||
| BS833_2 | 0.6% | ||||||
| BS839 | 24.2M | 21.4M | 88.6% | 20.3M | 83.8% | 1.2M | |
| BS839_1 | 0.6% | ||||||
| BS839_2 | 0.6% | ||||||
| BS840 | 20.3M | 17.3M | 84.9% | 16.2M | 79.9% | 1.0M | |
| BS840_1 | 0.5% | ||||||
| BS840_2 | 0.5% | ||||||
| BS847 | 25.7M | 19.9M | 77.3% | 18.2M | 70.5% | 1.7M | |
| BS847_1 | 0.5% | ||||||
| BS847_2 | 0.5% | ||||||
| BS848 | 21.4M | 19.4M | 90.5% | 18.5M | 86.6% | 0.8M | |
| BS848_1 | 0.5% | ||||||
| BS848_2 | 0.5% | ||||||
| BS849 | 21.4M | 15.7M | 73.2% | 14.9M | 69.4% | 0.8M | |
| BS849_1 | 0.8% | ||||||
| BS849_2 | 0.5% | ||||||
| BS855 | 20.4M | 17.3M | 85.0% | 16.4M | 80.6% | 0.9M | |
| BS855_1 | 0.5% | ||||||
| BS855_2 | 0.5% | ||||||
| BS856 | 21.6M | 19.6M | 91.1% | 18.8M | 87.3% | 0.8M | |
| BS856_1 | 0.4% | ||||||
| BS856_2 | 0.5% | ||||||
| BS857 | 21.2M | 19.0M | 89.5% | 18.1M | 85.3% | 0.9M | |
| BS857_1 | 0.5% | ||||||
| BS857_2 | 0.5% | ||||||
| BS862 | 23.2M | 21.0M | 90.5% | 20.2M | 86.9% | 0.8M | |
| BS862_1 | 0.5% | ||||||
| BS862_2 | 0.5% | ||||||
| BS863 | 22.6M | 18.9M | 83.6% | 17.7M | 78.3% | 1.2M | |
| BS863_1 | 0.5% | ||||||
| BS863_2 | 0.5% | ||||||
| BS864 | 24.7M | 17.9M | 72.5% | 17.0M | 68.7% | 0.9M | |
| BS864_1 | 0.8% | ||||||
| BS864_2 | 0.8% | ||||||
| BS865 | 38.6M | 34.2M | 88.7% | 32.8M | 85.0% | 1.4M | |
| BS865_1 | 0.5% | ||||||
| BS865_2 | 0.5% | ||||||
| BS870 | 20.2M | 18.2M | 90.3% | 17.4M | 86.2% | 0.8M | |
| BS870_1 | 0.5% | ||||||
| BS870_2 | 0.5% | ||||||
| BS871 | 25.3M | 16.1M | 63.7% | 15.3M | 60.5% | 0.8M | |
| BS871_1 | 0.5% | ||||||
| BS871_2 | 0.5% | ||||||
| BS872 | 25.5M | 22.2M | 86.9% | 21.2M | 82.9% | 1.0M | |
| BS872_1 | 0.5% | ||||||
| BS872_2 | 0.5% | ||||||
| BS873 | 21.8M | 18.7M | 86.0% | 17.8M | 81.5% | 1.0M | |
| BS873_1 | 0.5% | ||||||
| BS873_2 | 0.5% |
STAR
Universal RNA-seq aligner.URL: https://github.com/alexdobin/STARDOI: 10.1093/bioinformatics/bts635
Summary Statistics
Summary statistics from the STAR alignment
| Sample Name | Total reads | Aligned | Aligned | Uniq aligned | Uniq aligned | Multimapped | Avg. read len | Avg. mapped len | Splices | Annotated splices | GT/AG splices | GC/AG splices | AT/AC splices | Non-canonical splices | Mismatch rate | Del rate | Del len | Ins rate | Ins len |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| BS830 | 21.8M | 19.9M | 91.0% | 18.9M | 86.7% | 0.9M | 298.0bp | 291.7bp | 18.4M | 16.6M | 18.2M | 0.2M | 0.0M | 0.1M | 0.8% | 0.1% | 3.1bp | 0.0% | 3.2bp |
| BS831 | 22.2M | 20.6M | 92.5% | 19.7M | 88.3% | 0.9M | 298.0bp | 291.3bp | 18.6M | 16.7M | 18.3M | 0.2M | 0.0M | 0.1M | 0.8% | 0.1% | 3.1bp | 0.1% | 3.2bp |
| BS832 | 21.3M | 19.4M | 91.1% | 18.6M | 87.1% | 0.9M | 298.0bp | 291.6bp | 18.4M | 16.6M | 18.2M | 0.2M | 0.0M | 0.1M | 0.8% | 0.1% | 3.1bp | 0.0% | 3.2bp |
| BS833 | 20.6M | 18.9M | 91.8% | 18.1M | 88.0% | 0.8M | 298.0bp | 291.2bp | 17.3M | 15.6M | 17.1M | 0.2M | 0.0M | 0.1M | 0.8% | 0.1% | 3.1bp | 0.1% | 3.2bp |
| BS839 | 24.2M | 21.4M | 88.6% | 20.3M | 83.8% | 1.2M | 298.0bp | 290.3bp | 16.7M | 14.9M | 16.5M | 0.1M | 0.0M | 0.1M | 0.8% | 0.1% | 3.3bp | 0.1% | 3.5bp |
| BS840 | 20.3M | 17.3M | 84.9% | 16.2M | 79.9% | 1.0M | 298.0bp | 290.1bp | 12.4M | 11.0M | 12.3M | 0.1M | 0.0M | 0.1M | 0.8% | 0.1% | 3.3bp | 0.1% | 3.7bp |
| BS847 | 25.7M | 19.9M | 77.3% | 18.2M | 70.5% | 1.7M | 298.0bp | 290.6bp | 14.5M | 12.9M | 14.4M | 0.1M | 0.0M | 0.0M | 0.8% | 0.1% | 3.4bp | 0.1% | 3.7bp |
| BS848 | 21.4M | 19.4M | 90.5% | 18.5M | 86.6% | 0.8M | 298.0bp | 291.0bp | 16.5M | 14.7M | 16.3M | 0.1M | 0.0M | 0.0M | 0.8% | 0.1% | 3.3bp | 0.1% | 3.4bp |
| BS849 | 21.4M | 15.7M | 73.2% | 14.9M | 69.4% | 0.8M | 298.0bp | 291.2bp | 13.3M | 11.9M | 13.1M | 0.1M | 0.0M | 0.0M | 0.8% | 0.1% | 3.2bp | 0.1% | 3.4bp |
| BS855 | 20.4M | 17.3M | 85.0% | 16.4M | 80.6% | 0.9M | 298.0bp | 290.2bp | 12.8M | 11.4M | 12.6M | 0.1M | 0.0M | 0.1M | 0.9% | 0.1% | 3.3bp | 0.1% | 3.5bp |
| BS856 | 21.6M | 19.6M | 91.1% | 18.8M | 87.3% | 0.8M | 298.0bp | 290.3bp | 15.6M | 13.9M | 15.4M | 0.1M | 0.0M | 0.1M | 0.9% | 0.1% | 3.3bp | 0.1% | 3.5bp |
| BS857 | 21.2M | 19.0M | 89.5% | 18.1M | 85.3% | 0.9M | 298.0bp | 290.2bp | 14.4M | 12.9M | 14.2M | 0.1M | 0.0M | 0.1M | 0.9% | 0.1% | 3.3bp | 0.1% | 3.5bp |
| BS862 | 23.2M | 21.0M | 90.5% | 20.2M | 86.9% | 0.8M | 298.0bp | 290.5bp | 16.5M | 14.8M | 16.3M | 0.1M | 0.0M | 0.1M | 0.8% | 0.1% | 3.3bp | 0.1% | 3.5bp |
| BS863 | 22.6M | 18.9M | 83.6% | 17.7M | 78.3% | 1.2M | 298.0bp | 290.5bp | 14.8M | 13.2M | 14.6M | 0.1M | 0.0M | 0.1M | 0.8% | 0.1% | 3.3bp | 0.1% | 3.5bp |
| BS864 | 24.7M | 17.9M | 72.5% | 17.0M | 68.7% | 0.9M | 297.0bp | 289.4bp | 12.6M | 11.2M | 12.5M | 0.1M | 0.0M | 0.1M | 0.8% | 0.1% | 3.3bp | 0.1% | 3.6bp |
| BS865 | 38.6M | 34.2M | 88.7% | 32.8M | 85.0% | 1.4M | 298.0bp | 290.7bp | 29.8M | 26.7M | 29.4M | 0.3M | 0.0M | 0.1M | 0.8% | 0.1% | 3.3bp | 0.1% | 3.3bp |
| BS870 | 20.2M | 18.2M | 90.3% | 17.4M | 86.2% | 0.8M | 298.0bp | 290.5bp | 14.0M | 12.5M | 13.9M | 0.1M | 0.0M | 0.0M | 0.8% | 0.1% | 3.3bp | 0.1% | 3.5bp |
| BS871 | 25.3M | 16.1M | 63.7% | 15.3M | 60.5% | 0.8M | 298.0bp | 290.5bp | 12.7M | 11.4M | 12.5M | 0.1M | 0.0M | 0.0M | 0.8% | 0.1% | 3.4bp | 0.1% | 3.7bp |
| BS872 | 25.5M | 22.2M | 86.9% | 21.2M | 82.9% | 1.0M | 298.0bp | 290.6bp | 18.0M | 16.2M | 17.8M | 0.1M | 0.0M | 0.1M | 0.8% | 0.1% | 3.4bp | 0.1% | 3.5bp |
| BS873 | 21.8M | 18.7M | 86.0% | 17.8M | 81.5% | 1.0M | 298.0bp | 290.6bp | 14.3M | 12.9M | 14.2M | 0.1M | 0.0M | 0.0M | 0.8% | 0.1% | 3.3bp | 0.1% | 3.6bp |
Alignment Scores
Gene Counts
Statistics from results generated using --quantMode GeneCounts. The three tabs show counts for unstranded RNA-seq, counts for the 1st read strand aligned with RNA and counts for the 2nd read strand aligned with RNA.
Cutadapt
2.10
Finds and removes adapter sequences, primers, poly-A tails, and other types of unwanted sequences.URL: https://cutadapt.readthedocs.ioDOI: 10.14806/ej.17.1.200
Filtered Reads
This plot shows the number of reads (SE) / pairs (PE) removed by Cutadapt.
Trimmed Sequence Lengths (3')
This plot shows the number of reads with certain lengths of adapter trimmed for the 3' end.
Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length.
See the cutadapt documentation for more information on how these numbers are generated.
Software Versions
Software Versions lists versions of software tools extracted from file contents.
| Software | Version |
|---|---|
| Cutadapt | 2.10 |